One of the surprisingly frustrating moments in molecular modeling comes when you’re trying to intuitively edit a geometry — say, nudge an atom — and your software either resists or breaks the whole system. Traditional modeling tools often require repeated…

Before running a molecular dynamics simulation, equilibration is a critical step to prepare your system properly. But here’s the catch: many users—whether beginners or advanced—often spend unnecessary time managing input files and parameters for NVT equilibration. If you’re using the…

For molecular modelers exploring nanostructures, building carbon nanotube (CNT) models can often feel like a tedious and highly technical process. Whether you’re designing drug delivery systems, studying electronic properties, or simulating mechanical behavior at the nanoscale, getting the structure right…

When presenting molecular structures and mechanisms, clarity in camera movement can be the difference between a confusing animation and an insightful one. Molecular modelers often need to emphasize vertical changes—such as interactions across layers in a membrane protein or shifts…

Managing atom groups in molecular dynamics is crucial when preparing a simulation, especially when fine-tuning analysis protocols or defining dynamic groups like pull coordinates. One sticking point for many modelers is knowing when and how to add custom index groups…

When visualizing molecular designs, motion tells a powerful story—highlighting transitions, conformational shifts, or dynamic interactions with clarity that static images can’t match. But creating smooth, accurate animations can often seem like a hurdle, especially when working with molecular systems where…

When working with complex molecular structures, navigating a 3D environment efficiently can save time and effort. It’s common for molecular modelers to find themselves constantly adjusting the view—zooming into a reaction site, switching to a side angle, or stepping back…

As molecular modelers, we often work with many moving parts: molecular structures, scripts, analysis data, figures, and draft papers. Keeping all of these project components synchronized across machines—or sharing with collaborators—can become an organizational challenge. Fortunately, SAMSON‘s Universal File Embedding…

Tracking how ligands move through molecular systems — such as during unbinding or along diffusion pathways — is often a challenging task for molecular modelers. The movement can be complex, and visualizing it clearly across multiple frames of a trajectory…

Managing data in molecular modeling workflows can become overwhelming. Scripts, models, images, experimental results—these often reside in scattered folders across different machines. This increases the risk of broken references, version confusion, and forgotten dependencies. If you’re using SAMSON, the integrative…